A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models

J Chem Theory Comput. 2018 Feb 13;14(2):1071-1082. doi: 10.1021/acs.jctc.7b01004. Epub 2018 Jan 24.


Markov state models (MSMs) are a powerful framework for the analysis of molecular dynamics data sets, such as protein folding simulations, because of their straightforward construction and statistical rigor. The coarse-graining of MSMs into an interpretable number of macrostates is a crucial step for connecting theoretical results with experimental observables. Here we present the minimum variance clustering approach (MVCA) for the coarse-graining of MSMs into macrostate models. The method utilizes agglomerative clustering with Ward's minimum variance objective function, and the similarity of the microstate dynamics is determined using the Jensen-Shannon divergence between the corresponding rows in the MSM transition probability matrix. We first show that MVCA produces intuitive results for a simple tripeptide system and is robust toward long-duration statistical artifacts. MVCA is then applied to two protein folding simulations of the same protein in different force fields to demonstrate that a different number of macrostates is appropriate for each model, revealing a misfolded state present in only one of the simulations. Finally, we show that the same method can be used to analyze a data set containing many MSMs from simulations in different force fields by aggregating them into groups and quantifying their dynamical similarity in the context of force field parameter choices. The minimum variance clustering approach with the Jensen-Shannon divergence provides a powerful tool to group dynamics by similarity, both among model states and among dynamical models themselves.

MeSH terms

  • Algorithms
  • Markov Chains*
  • Molecular Dynamics Simulation*
  • Protein Folding
  • Proteins / chemistry*


  • Proteins